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BIOCH 590: Biomacromolecules Spring 2010

Copyright: Jianhan Chen 456(7&,'3,'(.3%'( 8(

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Discovery of DNA Structure and Function: Watson and Crick, L. A. Pray, Nature Education 1 (2008).

Watson, J. D., & Crick, F. H. C. A structure for deoxyribose nucleic acid. Nature 171, 737–738 (1953)

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First X-ray protein structures Hemoglobin and myoglobin, by Max Perutz and Sir John Kendrew, respectively, in 1958

Source: PDB

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http://www.bfsc.leidenuniv.nl/teaching

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Try over 300 conditions is probably enough to tell whether it will even crystallize?

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Roderick MacKinnon Nobel Prize in Chemistry 2003

KcsA (PDB: 1r3j) MacKinnon, Nature (2002).

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International symbol (Herman-Mauguin symbol): shortest symbols to general all symmetry elements e.g., P3121 P: lattice centering type (primitive) 31: symmetry of primary axis

(trigonal c-axis) 2: symmetry of secondary axis (2 fold) 1: symmetry of tertiary axis

Restriction of chirality: 65 space groups for biomolecules!

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A single recording of diffraction, i.e., a single reflection, at a fixed crystal orientation only sample a limited number of reciprocal lattice points!

Systematically rotating (a precisely aligned) crystal allows all reciprocal lattice to be sampled (precession imaging).

Intensities of the reflections vary dramatically, which is related to the types and positions of atoms within the unit cell.

http://xray0.princeton.edu/~phil/Facility/Guides/XrayDataCollection.html

Indexing 1!

Cell lengths (Angstrom): 6.4232 7.3423 15.7870!Cell angles (degree): 95.8000 96.5907 102.5697!…!

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j=1

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# fj: atomic scattering factor (Xj,Yj,Zj): fractional cell coordinates

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h,k,l% ": “the electron density”

amplitude (known) phase (unknown)

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Structural factor data F(h,k): inner circle marks 2A resolution. Including additional data up to the outer circle increases resolution to 1A (Fig 12.16 of Tinoco)

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A 2.6 Å SIR electron-density map with the final C% trace of the structure superimposed.

Phase probability for one reflection in a MIR experiment. (a) One derivative. (b) Three derivatives.

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http://www.sci.sdsu.edu/TFrey/Bio750/Bio750X-Ray.html

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Correlation between loop 7 B factor and kcat in PTE variants

bacterial phosphotriesterase (PTE)

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PDB Molecule of the Month:

Enhanceosome

PDB: 1t2k, 2pi0, 2o6g and 2o61

Panne et al, Embo J. (2004)

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NMR X-ray crystallography

short time scale, protein folding long time scale, static structure solution, purity single crystal, purity < 20kD, domain any size, domain, complex functional active site active or inactive atomic nuclei, chemical bonds electron density resolution limit 2-3.5Å resolution limit 1.5-3.5Å

Dynamics Transient interactions